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- PDB-4c8k: Crystal structure of the large fragment of DNA polymerase I from ... -

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Basic information

Entry
Database: PDB / ID: 4c8k
TitleCrystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a partially closed complex with the artificial base pair d5SICS-dNaMTP
Components
  • 5'-D(*AP*AP*C*LHOP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'
  • 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*C*DOC)-3'
  • DNA POLYMERASE I, THERMOSTABLE
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / UNNATURAL NUCLEOTIDE / ARTIFICIAL NUCLEOTIDE / BINARY COMPLEX / KLENTAQ
Function / homology
Function and homology information


nucleoside binding / hydrolase activity, acting on ester bonds / double-strand break repair via alternative nonhomologous end joining / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Taq polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 ...Taq polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / PIN-like domain superfamily / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-BMR / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.17 Å
AuthorsBetz, K. / Malyshev, D.A. / Lavergne, T. / Welte, W. / Diederichs, K. / Romesberg, F.E. / Marx, A.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Structural Insights Into DNA Replication without Hydrogen Bonds.
Authors: Betz, K. / Malyshev, D.A. / Lavergne, T. / Welte, W. / Diederichs, K. / Romesberg, F.E. / Marx, A.
History
DepositionOct 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Atomic model / Database references
Revision 2.0Aug 23, 2017Group: Atomic model / Data collection / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / refine / reflns / reflns_shell
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _refine.pdbx_method_to_determine_struct / _refine.pdbx_starting_model / _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE I, THERMOSTABLE
B: 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*C*DOC)-3'
C: 5'-D(*AP*AP*C*LHOP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3889
Polymers69,5193
Non-polymers8696
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-23.7 kcal/mol
Surface area25930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.039, 115.039, 91.106
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA POLYMERASE I, THERMOSTABLE / TAQ POLYMERASE 1 / LARGE FRAGMENT OF TAQ DNA POLYMERASE I


Mass: 60936.965 Da / Num. of mol.: 1 / Fragment: KLENOW FRAGMENT, RESIDUES 293-832
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Plasmid: PGDR11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19821, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*C*DOC)-3'


Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PRIMER' / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*AP*AP*C*LHOP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'


Mass: 4964.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TEMPLATE / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 5 types, 150 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-BMR / ((2R,3S,5R)-3-hydroxy-5-(3-methoxynaphthalen-2-yl)methyl-tetrahydrogen-triphosphate / dNaM-Triphosphate


Mass: 514.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21O13P3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details5'-AA OF THE TEMPLATE IS NOT RESOLVED IN THE STRUCTURE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.58 % / Description: NONE
Crystal growpH: 7
Details: 15% W/V PEG 8000, 100MM TRIS PH 7.0, 200MM MAGNESIUM FORMIAT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2012 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.16→48.6 Å / Num. obs: 34375 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 42.06 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.44
Reflection shellResolution: 2.16→2.29 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 0.47 / CC1/2: 0.478 / % possible all: 51.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3m8s

3m8s


Resolution: 2.17→48.637 Å / SU ML: 0.25 / σ(F): 16.32 / Phase error: 26.44 / Stereochemistry target values: ML / Details: RESIDUES 643-660 HAVE HIGH B- -FACTORS
RfactorNum. reflection% reflection
Rfree0.2214 1671 5 %
Rwork0.1811 --
obs0.1832 33357 89.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.15 Å2
Refinement stepCycle: LAST / Resolution: 2.17→48.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 530 54 144 5019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075049
X-RAY DIFFRACTIONf_angle_d0.876944
X-RAY DIFFRACTIONf_dihedral_angle_d16.8691970
X-RAY DIFFRACTIONf_chiral_restr0.034757
X-RAY DIFFRACTIONf_plane_restr0.004824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.23390.3339720.36461602X-RAY DIFFRACTION99
2.2339-2.3060.3744560.2991987X-RAY DIFFRACTION98
2.306-2.38840.29011460.22612914X-RAY DIFFRACTION100
2.3884-2.4840.25871290.21052948X-RAY DIFFRACTION100
2.484-2.5970.25241540.20992910X-RAY DIFFRACTION100
2.597-2.73390.24061610.20812906X-RAY DIFFRACTION100
2.7339-2.90520.26631510.20942929X-RAY DIFFRACTION100
2.9052-3.12950.25811760.22262936X-RAY DIFFRACTION100
3.1295-3.44440.25561420.192936X-RAY DIFFRACTION100
3.4444-3.94260.20921410.16692569X-RAY DIFFRACTION87
3.9426-4.96640.18161720.14152972X-RAY DIFFRACTION100
4.9664-48.64940.18281710.1573077X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9109-0.5436-0.22961.5411-0.2120.9151-0.1146-0.0046-0.3103-0.1263-0.019-0.10230.31770.1056-00.5005-0.05370.05430.2709-0.00420.320242.8379-45.8972-17.8253
20.84680.1014-0.22020.23370.19361.41570.01020.00020.3215-0.07270.0466-0.0099-0.20360.06310.00060.383-0.0692-0.00510.2470.00490.424434.0662-16.9066-3.4864
30.05430.04340.11260.03940.07740.1205-0.08330.0236-0.0001-0.14530.01490.0269-0.7811-0.3824-01.00820.11890.00710.69120.11120.75318.5903-14.2162-7.066
41.353-0.0253-0.49130.4536-0.19671.1973-0.09110.05610.0144-0.04340.00830.0730.0084-0.210400.3663-0.0835-0.03760.30370.02290.287218.7319-28.1173-11.6038
50.01780.0716-0.10240.0739-0.18130.2176-0.25970.3216-0.06490.3479-0.1570.1643-0.56420.5374-0.01930.3654-0.02680.00240.47890.04680.41240.7262-26.28515.3644
60.05840.0221-0.26450.37120.35170.4301-0.3342-0.0866-0.17570.11760.2414-0.14970.18890.13750.00010.38120.0023-0.01410.38220.00310.342836.985-26.79465.7586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 293 THROUGH 433 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 434 THROUGH 633 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 634 THROUGH 671 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 672 THROUGH 832 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 101 THROUGH 111 )
6X-RAY DIFFRACTION6CHAIN C AND (RESID 203 THROUGH 216 )

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